Certain monoclonal antibodies have therapeutic potential against a particular disease, even though similar antibodies seldom or never arise during disease progression in most humans. For example, in models of HIV infection antibody 2G12 is known to neutralize a broad range of HIV strains and protect rhesus macaques, but 2G12-like antibodies are rarely produced in HIV-positive humans. In such cases, a “reverse immunology” approach would be desirable, in which an immunogen is designed which structurally mimics the epitope of the therapeutically useful monoclonal antibody. Immunization with this epitope mimic would then elicit an antibody response mimicking the monoclonal antibody.
The success of this strategy depends on the extent to which one can design a molecule that is a good structural and conformational mimic of the native epitope. This goal requires a good structural or conformational understanding of the epitope structure. “Carbohydrate epitopes” are epitopes in which a carbohydrate is a necessary component for antibody binding. However, the antibody-epitope binding interaction is rarely understood at the atomic structural level and, in most cases, it is not known whether the antibody binds to structural features neighboring the carbohydrate in addition to the carbohydrate itself. Moreover, carbohydrates are flexible and may exhibit different conformational profiles when attached to structures other than those present in the actual target protein.
For example, the majority of HIV vaccine approaches to date have tested either HIV protein subunits or peptides, and/or caused the host to make these proteins by intracellular delivery of HIV DNA using viral vectors or gold particles. Because a broadly-neutralizing antibody, 2G12, binds to a cluster of carbohydrates on the viral envelope protein gp120, a few groups have designed and tested synthetically clustered carbohydrate immunogens in an attempt to mimic the 2G12 epitope and thus elicit 2G12-like antibodies. In these approaches, the backbones linking the carbohydrates were flexible organic chains or cyclic peptides that were easy to synthesize. No study has described an attempt to mimic in an exact way the natural backbone in which the carbohydrates are embedded. The choice of backbone is key; due to the flexibility of carbohydrates, their conformation, spacing, and orientation is undoubtedly influenced by the surfaces they are embedded within, and the flexible carbohydrate cluster immunogens designed to date have not achieved true conformational mimicry of the epitope. The choice of backbone is also important because the peptide structures of gp120 in which the carbohydrates are embedded are likely make some contact with 2G12 and comprise part of the epitope.
Further, other important information regarding 2G12 binding to HIV remains unknown, including: precisely which oligomannans on the gp120 surface are bound by the antibody; whether the antibody also binds to polypeptide surface residues; and how the oligomannans are conformationally supported by the protein. Synthetic clusters of oligomannans mounted on non-natural designed scaffolds have so far failed to elicit 2G12-like antibodies, possibly because such epitope mimics do not adequately resemble the native epitope. Even with perfect structural knowledge of an epitope, a priori design of antigens that faithfully mimic its structure is currently impossible.
Additionally, a major limitation of RNA and DNA aptamers is that the nucleotide building blocks are limited to the naturally occurring bases and close analogues that act as substrates for DNA or RNA polymerases. The utility of the oligonucleotide framework, and the power of the selection process, could be greatly extended if the bases could be more extensively modified.